I am running the following command to index my genome:
STAR --runThreadN 8 --runMode genomeGenerate --genomeDir output/index/star --genomeFastaFiles ref.fa --sjdbGTFfile ref.gff3 --sjdbGTFtagExonParentTranscript Parent --sjdbOverhang 100
and I get the following output:
Feb 27 10:27:37 ..... started STAR run Feb 27 10:27:37 ... starting to generate Genome files Feb 27 10:27:40 ... starting to sort Suffix Array. This may take a long time... Feb 27 10:27:42 ... sorting Suffix Array chunks and saving them to disk... Feb 27 10:28:26 ... loading chunks from disk, packing SA... Feb 27 10:28:30 ... finished generating suffix array Feb 27 10:28:30 ... generating Suffix Array index terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc
Searches for the GNU/Linux error lead to some pages about C++ that I don't understand.
Submitting it as a batch job works fine but I would like to know why it does not work on a node. It is quite practical for me to test small code like this without submitting a batch job.
The command above works fine on my laptop running Mac OSX.
The STAR version is STAR_2.5.3a on both computers: STAR_2.5.3a
The memory usage of the node is the following:
total used free shared buffers cached 251 251 0 0 0 232
so, is there 0 memory for me to use on this node?
Why is my indexing aborting?